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BMRB: 15192

2JOR

NMR Solution Structure, Stability, and Interaction of the Recombinant Bovine Fibrinogen alphaC-Domain Fragment

Authors

Burton, R.A., Tsurupa, G., Roy, H., Nico, T., Leonid, M.

Assembly

alphaC-Domain Fragment

Entity

1. alphaC-Domain Fragment (polymer, Thiol state: all disulfide bound), 79 monomers, 8959.549 Da Detail

MIDNEKVTSG HTTTTRRSCS KVITKTVTNA DGRTETTKEV VKSEDGSDCG DADFDWHHTF PSRGNLDDFF HRDKDDFFT

Formula weight

8959.549 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS19:SG	1:CYS49:SG

Source organism

Bos taurus

Exptl. method

solution NMR

Refine. method

distance geometry, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 47.1 %, Completeness (bb): 74.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	47.1 % (411 of 873)	41.7 % (187 of 448)	43.7 % (150 of 343)	90.2 % (74 of 82)
Backbone	74.2 % (350 of 472)	78.4 % (127 of 162)	64.2 % (149 of 232)	94.9 % (74 of 78)
Sidechain	28.0 % (133 of 475)	21.3 % (61 of 286)	38.9 % (72 of 185)	0.0 % (0 of 4)
Aromatic	0.0 % (0 of 88)	0.0 % (0 of 44)	0.0 % (0 of 43)	0.0 % (0 of 1)
Methyl	11.3 % (7 of 62)	12.9 % (4 of 31)	9.7 % (3 of 31)

1. subunit 1

MIDNEKVTSG HTTTTRRSCS KVITKTVTNA DGRTETTKEV VKSEDGSDCG DADFDWHHTF PSRGNLDDFF HRDKDDFFT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 282 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	150 uM
2	KPO4	natural abundance	10 mM
3	NaCl	natural abundance	150 mM
4	D20	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JOR, Strand ID: A Detail

Release date

2007-09-11

Citation

NMR solution structure, stability, and interaction of the recombinant bovine fibrinogen alphaC-domain fragment
Burton, R.A., Tsurupa, G., Hantgan, R.R., Tjandra, N., Medved, L.
Biochemistry (2007), 46, 8550-8560, PubMed 17590019 , DOI 10.1021/bi700606v , Abstract

Related entities 1. alphaC-Domain Fragment, : 1 : 2 : 7 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15192_2jor.nef
Input source #2: Coordindates	2jor.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:19:CYS:SG	A:49:CYS:SG	oxidized, CA 55.119, CB 42.245 ppm	oxidized, CA 56.481, CB 40.332 ppm	2.022

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70---------
MIDNEKVTSGHTTTTRRSCSKVITKTVTNADGRTETTKEVVKSEDGSDCGDADFDWHHTFPSRGNLDDFFHRDKDDFFT
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MIDNEKVTSGHTTTTRRSCSKVITKTVTNADGRTETTKEVVKSEDGSDCGDADFDWHHTFPSRGNLDDFFHRDKDDFFT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	79	0	0	100.0

Content subtype: combined_15192_2jor.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	397		100.0 (chain: A, length: 79)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	420 (1)	noe	77.2 (chain: A, length: 79)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	22 (1)	hbond	13.9 (chain: A, length: 79)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	50 (50)	.	44.3 (chain: A, length: 79)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	32 (32)	.	40.5 (chain: A, length: 79)
2	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	39 (39)	.	49.4 (chain: A, length: 79)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 175
  - ¹³C chemical shifts: 148
  - ¹⁵N chemical shifts: 74
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	448	175	39.1
¹³C chemical shifts	343	148	43.1
¹⁵N chemical shifts	87	74	85.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	162	123	75.9
¹³C chemical shifts	158	77	48.7
¹⁵N chemical shifts	78	74	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	286	52	18.2
¹³C chemical shifts	185	71	38.4
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	3	9.4
¹³C chemical shifts	32	2	6.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	0	0.0
¹³C chemical shifts	43	0	0.0
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 77.2%
- Total number of restraints: 420
- Weight of restraints: 1.0 (420)
- Potential type of restraints: square-well-parabolic (420)
- Range of distance target values: 1.8, 5.6 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 13.9%
  - Total number of restraints: 22
  - Weight of restraints: 1.0 (22)
  - Potential type of restraints: square-well-parabolic (22)
  - Range of distance target values: 2.0, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 44.3%
- Total number of restraints: 50
- Total number of restraints per polymer type: 50
- Weight of restraints: 1.0 (50)
- Potential type of restraints: square-well-parabolic (50)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 40.5%
- Total number of restraints: 32
- Potential type of restraints: square-well-parabolic (32)
- Range of observed RDC values: -16.03, 23.26 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
- Saveframe: CNS/XPLOR_dipolar_coupling_4
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 49.4%
  - Total number of restraints: 39
  - Potential type of restraints: square-well-parabolic (39)
  - Range of observed RDC values: -26.45, 32.45 (Hz)
  - Histogram of observed RDC values
  - RDC restraints per residue

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Found 1 Document (0.67 seconds)

BMRB: 15192

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. alphaC-Domain Fragment, : 1 : 2 : 7 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

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Sample

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Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail